Cellular and extracellular siderophores of Aspergillus nidulans and Penicillium chrysogenum

Aspergillus nidulans and Penicillium chrysogenum produce specific cellular siderophores in addition to the well-known siderophores of the culture medium. Since this was found previously in Neurospora crassa, it is probably generally true for filamentous ascomycetes. The cellular siderophore of A. nidulans is ferricrocin; that of P. chrysogenum is ferrichrome. A. nidulans also contains triacetylfusigen, a siderophore without apparent biological activity. Conidia of both species lose siderophores at high salt concentrations and become siderophore dependent. This has also been found in N. crassa, where lowering of the water activity has been shown to be the causal factor. We used an assay procedure based on this dependency to reexamine the extracellular siderophores of these species. During rapid mycelial growth, both A. nidulans and P. chrysogenum produced two highly active, unidentified siderophores which were later replaced by a less active or inactive product--coprogen in the case of P. chrysogenum and triacetylfusigen in the case of A. nidulans. N. crassa secreted coprogen only. Fungal siderophore metabolism is varied and complex

The action of certain substituted phenols on marine eggs in relation to their dissociation

It has been shown by Clowes and Krahl (1, 2) that various substituted phenols as well as dinitrophenol increase the respiratory rate of marine eggs. Also, the highly interesting reversible block to cleavage, which they found to occur at the maximum of respiratory stimulation, is likewise exhibited. The different substances (nitro- and halo-phenols and cresols in particular) used were found to be active in different concentrations, and some attempt is made to relate the activity to molecular structure. The degree of dissociation of the phenolic OH is taken to be of no significance in their experiments. There has been some controversy concerning this question. Field, Martin and Field (3, 4) showed that in yeast the amount of respiratory stimulation by 2,4-dinitrophenol and by 4,6-dinitrocresol depends upon the concentration of the undissociated form present, similar calculated concentrations of undissociated DNP giving at different pH's the same stimulation. Citing their own experiments and those of Ehrenfest and Ronzoni (5) on yeast, De Meio and Barron (6), on the other hand, disagree with this conclusion

Gravitational quasinormal modes for Anti-de Sitter black holes

Quasinormal mode spectra for gravitational perturbations of black holes in four dimensional de Sitter and anti-de Sitter space are investigated. The anti-de Sitter case is relevant to the ADS-CFT correspondence in superstring theory. The ADS-CFT correspondence suggests a prefered set of boundary conditions.Comment: 12 pages, 6 figures in ReVTe

d+idd+id Holographic Superconductors

A holographic model of $d+id$ superconductors based on the action proposed by Benini, Herzog, and Yarom [arXiv:1006.0731] is studied. This model has a charged spin two field in an AdS black hole spacetime. Working in the probe limit, the normalizable solution of the spin two field in the bulk gives rise to a $d+id$ superconducting order parameter at the boundary of the AdS. We calculate the fermion spectral function in this\ superconducting background and confirm the existence of fermi arcs for non-vanishing Majorana couplings. By changing the relative strength $\gamma$ of the $d$ and $id$ condensations, the position and the size of the fermi arcs are changed. When $\gamma =1$, the spectrum becomes isotropic and the spectral function is s-wave like. By changing the fermion mass, the fermi momentum is changed. We also calculate the conductivity for these holographic $d+id$ superconductors where time reversal symmetry has been broken spontaneously. A non-vanishing Hall conductivity is obtained even without an external magnetic field.Comment: 24 pages,17 figures, Add more discussions on hall conductivity, two new figures, Matched with published versio

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Numerical Relativity: A review

Computer simulations are enabling researchers to investigate systems which are extremely difficult to handle analytically. In the particular case of General Relativity, numerical models have proved extremely valuable for investigations of strong field scenarios and been crucial to reveal unexpected phenomena. Considerable efforts are being spent to simulate astrophysically relevant simulations, understand different aspects of the theory and even provide insights in the search for a quantum theory of gravity. In the present article I review the present status of the field of Numerical Relativity, describe the techniques most commonly used and discuss open problems and (some) future prospects.Comment: 2 References added; 1 corrected. 67 pages. To appear in Classical and Quantum Gravity. (uses iopart.cls